[color=#000000]Hi Sascha,[/color]
[color=#000000]To run the entire preprocessing pipeline using batch commands simply add the line:[/color]
[color=#000000] batch.Setup.preprocessing.steps = 'default_mni';[/color]
[color=#000000]to your batch structure (note: do not use the batch.New fields, that functionality is obsolete, instead simply enter your functional data in the batch.Setup.functionals field and your structural data in the batch.Setup.structurals field as usual, and simply add the line above to run the standard preprocessing pipeline; see [i]help conn_batch[/i] for additional details)[/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[color=#000000]
[/color][i]Originally posted by Sascha Froelich:[/i][quote]Hello everyone,
I am trying to write a BATCH script that preprocesses my data like the default preprocessing pipeline does. While there appears to be no command that does all of the comprised preprocessing steps at once, I could specify them one by one in BATCH.New.steps. However, in the conn batchscripting manual there seems to be no command for, e.g., Outlier Detection & Scrubbing, etc. ...
Probably I just overlooked something, however this is the question: How do I send my data through the "default preprocessing pipeline" with BATCH commands?
Any help is highly appreciated!
Kind regards,
Sascha[/quote]
[color=#000000]To run the entire preprocessing pipeline using batch commands simply add the line:[/color]
[color=#000000] batch.Setup.preprocessing.steps = 'default_mni';[/color]
[color=#000000]to your batch structure (note: do not use the batch.New fields, that functionality is obsolete, instead simply enter your functional data in the batch.Setup.functionals field and your structural data in the batch.Setup.structurals field as usual, and simply add the line above to run the standard preprocessing pipeline; see [i]help conn_batch[/i] for additional details)[/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[color=#000000]
[/color][i]Originally posted by Sascha Froelich:[/i][quote]Hello everyone,
I am trying to write a BATCH script that preprocesses my data like the default preprocessing pipeline does. While there appears to be no command that does all of the comprised preprocessing steps at once, I could specify them one by one in BATCH.New.steps. However, in the conn batchscripting manual there seems to be no command for, e.g., Outlier Detection & Scrubbing, etc. ...
Probably I just overlooked something, however this is the question: How do I send my data through the "default preprocessing pipeline" with BATCH commands?
Any help is highly appreciated!
Kind regards,
Sascha[/quote]